Signaling Mechanisms in Renal Compensatory Hypertrophy Revealed by
Multi-Omics
Hiroaki Kikuchi, Chun-Lin Chou,
Chin-Rang Yang, Lihe Chen, Hyun Jun Jung, Kavee Limbutara,
Benjamin Carter, Zhi-Hong Yang, Julia Kun, Alan T. Remaley and Mark A. Knepper
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Available code
## RNA seq
Example
code for file processing for RNA seq in UNIX system in Biowulf in NIH
Example
code for differential expression analysis in R (EdgeR and DEseq2)
## ATAC seq
Example code for file processing for ATAC seq in UNIX system in
Biowulf in NIH
Example code for differential peak analysis in R (Diffbind)
Example code for quality control and footprinting
analysis in R (ATACseqQC)
Supplementary
Data
Supplementary Data 1. Raw data
of kidney weight and body weight in mice without (Sham) or with unilateral
nephrectomy (UNx) at different time points (Days 1,
Day 3, and 30).
Supplementary Data 2.
Histological analysis of kidney from mice without (Sham) or with unilateral
nephrectomy (UNx) surgery at the 72 h timepoint.
Supplementary Data 3.
Morphological data of IF-stained microdissected S1
proximal tubules and cortical collecting duct (CCD) 30 days after surgery.
Supplementary Data 4. The
hypothesis signaling pathways in kidney triggered by unilateral nephrectomy.
Supplementary Data 5. The
enriched TF binding motifs identified by HOMER de novo motif analysis in
chromatin regions that are more accessible in UNx
(DAR-UP), those that are less accessible in UNx
(DAR-down),
and all chromatin
regions that are identified in S1 segment of the proximal tubule.
Supplementary Data 6. A
quantitative comparison of chromatin accessibility in microdissected
S1 segment of proximal tubules at 24 h
after UNx. (ATAC-seq
in PT-S1 at 24 h)
Supplementary Data 7. Target
gene sets for individual transcription factors listed in Supplementary Table
1.
Supplementary Data 8. Summary of
transcription factor target gene sets analysis for ATAC-seq data (24h proximal
tubule), RNA-seq data for proximal tubules at 24 h and 72 h after surgery.
Supplementary Data 9. Transcript
abundance changes in microdissected S1 segment of PTs
of mice at 24 h after UNx. (RNA-seq in PT-S1 at 24 h)
Supplementary Data 10. Upstream
regulator analysis using QIAGEN’s Ingenuity Pathway Analysis for S1 proximal
tubule RNA-seq dataset at the 24h timepoint.
Supplementary Data 11. Transcript
abundance changes in microdissected CCDs of mice at
24 h after UNx. (RNA-seq
in CCD at 24 h)
Supplementary Data 12. Transcript
abundance changes in microdissected CCDs of mice at
72 h after UNx. (RNA-seq
in CCD at 72 h)
Supplementary Data 13. Transcript
abundance changes in microdissected S1 segment of PTs
of mice at 72 h after UNx. (RNA-seq in PT-S1 at 72 h)
Supplementary Data 14. Comparison
of the core enrichments of genes annotated as either “G2M CHECKPOINT” or
“E2F_TARGET” between S1 proximal tubule RNA seq at the 72 hour time point and
CCD RNA seq at the 24 hour timepoint.
Supplementary Data 15. Upstream regulator analysis using QIAGEN’s Ingenuity Pathway
Analysis for S1 proximal tubule RNA-seq dataset at the 72 h timepoint.
Supplementary Data 16. Protein
abundance changes in whole kidney of mice at 24 h after UNx.
Supplementary Data 17. Upstream
regulator analysis using QIAGEN’s Ingenuity Pathway Analysis for whole kidney
proteomics dataset at the 24 h timepoint. (Whole-kid
proteomics at 24 h)
Supplementary Data 18. Protein
abundance changes in kidney cortex of mice at 24 h after UNx.
(CORTEX proteomics at 24 h)
Supplementary Data 19. Upstream
regulator analysis using QIAGEN’s Ingenuity Pathway Analysis for kidney cortex
proteomics dataset at the 24 h timepoint.
Supplementary Data 20. Protein
abundance changes in whole kidney of mice at 72 h after UNx.
(Whole-kid proteomics at 72 h)
Supplementary Data 21. Upstream regulator analysis using QIAGEN’s Ingenuity Pathway
Analysis for whole kidney proteomics dataset at the 72 h timepoint.
Supplementary Data 22.
Phosphoprotein abundance changes in whole kidney of mice at 24 h after UNx. (Whole-kid PHOSPHOproteomics at 24 h)
Supplementary Data 23.
Phosphoprotein abundance changes in whole kidney of mice at 72 h after UNx. (Whole-kid PHOSPHOproteomics at 72 h)
Supplementary Data 24. Protein
kinases that underwent changes in phosphorylation in contralateral kidney in
response to unilateral nephrectomy (UNx) relative to
sham surgery at 72 h.
Supplementary Data 25. Data
integration analysis using multi-omics datasets.
Supplementary Data 26. The
changes of abundance of amino acid transporters in transcriptome and proteome.
Supplementary Data 27. Fatty acid
(Gas chromatography) and lipid analysis (calorimetric assay) of kidney from
Sham or UNx at 24 hour after surgery.
Supplementary Data 28. Body
weight, kidney weight and histological parameters of the kidney from mice
without (Vehicle) and with fenofibrate treatments for 14 days.
Supplementary Data 29.
Morphological data of IF-stained microdissected S1
proximal tubules from mice without (vehicle) and with fenofibrate treatments
for 14 days.
Supplementary Data 30. Cell size
are (µm2)
assay using liver in mice without (Vehicle) or with fenofibrates treatments for
14 days using NDP Nanozoomer.
Supplementary Data 31.
Morphological data of IF-stained microdissected S1
proximal tubules from WT mice or PPARα -/- mice 3 days after unilateral
nephrectomy.
Webpage created by Hiroaki
Kikuchi and Mark Knepper in the Epithelial Systems Biology Laboratory (Mark Knepper,
Chief) at the National Heart, Lung and Blood Institute as part of
its Kidney Systems Biology Project. (Aug 2022, revised Jan 2023)